Different doses (1%, 5%, 10%, mass fraction) of animal manure compost were added into a multi-heavy metal contaminated paddy soil for 150 d, and the changes in microbial structure and composition were evaluated. Compost exhibited dose-dependent effects on the rhizosphere bacterial community. Low (1%) and middle (5%) additions of compost exerted more distinct influence on bacterial community structure in rhizosphere soil than in bulk soil. The bacterial diversity after addition of compost decreased in rhizosphere soils compared with that in bulk soil. Results of redundancy analysis (RDA) indicated that different responses of rhizosphere and non-rhizosphere bacterial community to the changed soil physicochemical properties (soil pH, Pb, Cd and Cu levels) might be one reason for the differences. Thus, in agricultural management practice, the influence of compost on rhizosphere microbes should be considered.